trim_paired now can work on a combined input file

Instead of having files separate ("*.PE.1.fastq" and "*.PE.2.fastq"),
you can have a single combined input file where the reads are already
interleaved.

Added a test directory and some test fastq files.

Added a .gitignore mask
Added a .gitignore
updated usage messages and fixed param logic
Merge branch 'combined_input'
updated markdown readme
Merge pull request #6 from bcthomas/master

altered to work with combined paired-end input files